A Raman Spectroscopic and Computational Study of the Effects of Halogen Bonding on Pyrimidine Containing Systems

Reves, Peyton Lindsey
(2015)
A Raman Spectroscopic and Computational Study of the Effects of Halogen Bonding on Pyrimidine Containing Systems.
Undergraduate thesis,
under the direction of Nathan Hammer from
Chemistry,
University of Mississippi.

Abstract

This thesis involves the study of the effects of halogen bonding on pyrimidine containing systems. Halogen bonding is a type of non-covalent interaction that can occur when a Lewis base interacts with an iodine, bromine, or chlorine atom in a second molecule. The phenomenon of halogen bonding is explained by the presence of a localized region of positive electrostatic potential that exists on the halogen. This positive region is referred to as the σ-hole, and gives halogen bonding its other common name, σ-hole bonding. The magnitude of the positive σ-hole depends on both the type of halogen molecule involved in the interaction as well as the characteristics of the molecule to which the halogen is bonded. The strength of the halogen bond tends to increase from chlorine < bromine < iodine. The careful and directed use of this intermolecular interaction has been suggested for use in several areas of supramolecular chemistry. For example, halogen bonding has been employed in crystal engineering as a means of forming new types of crystals. In this work, halogen bonding interactions between a nitrogen-containing heterocyclic biological building block (pyrimidine) and aryl halides are studied both experimentally and theoretically. Experimental Raman spectra of liquid mixtures are compared to the results of electronic structure calculations on halogen bond containing molecular clusters. Mixtures pyrimidine with bromobenzene, iodobenzene, bromopentafluorobenzene, and iodopentafluorobenzene were examined both experimentally and theoretically. Results indicate that the addition of electron withdrawing fluorine atoms strengthen the halogen bond interaction, leading to significant blue shifts in a number of pyrimidine’s normal modes in mixtures of iodopentafluorobenzene and pyrimidine, similar to the shifts induced by hydrogen bonding between pyrimidine and water. Additionally, a co-crystal containing halogen bonds is characterized using micro-Raman spectroscopy and compared to theoretical calculations of the co-crystal complex. Though only small shifts in vibrational modes were observed in the co-crystal, theory and experiment proved to agree very well. An X-Ray crystal structure of the co-crystal, however, confirmed the presence of halogen bonds in the crystal.